fix(github-app): preserve gate blocking defaults

[JSONbored]

Motivation

• Prevent silent policy bypass introduced by migrating linked_issue_gate_mode and duplicate_pr_gate_mode to advisory, which caused formerly required Gate checks to become non-blocking after upgrade.
• Restore prior merge hygiene behavior for repositories that had gateCheckMode enabled without requiring an operator change.

Description

• Change DB migration and schema defaults for linked_issue_gate_mode and duplicate_pr_gate_mode from advisory back to block by updating migrations/0023_gate_quality_modes.sql and src/db/schema.ts.
• Add a follow-up migration migrations/0025_restore_gate_blocking_modes.sql that updates existing repository_settings rows to restore block for those fields when gate_check_mode = 'enabled'.
• Update runtime/default handling in src/db/repositories.ts and API parsing defaults in src/api/routes.ts so omitted settings preserve legacy blocking behavior (default to block when not explicitly set).
• Make gate evaluation treat omitted per-rule modes as legacy block by default in src/rules/advisory.ts while still honoring explicit advisory and off values, and update Gate check copy in src/github/app.ts and unit tests to reflect the preserved behavior.

Testing

• Ran targeted unit tests with vitest for rules, GitHub app, and queue: all targeted tests passed.
• Ran full unit test suite with npm run test:unit: all unit tests passed.
• Ran type checking with tsc --noEmit and OpenAPI generation check with the UI openapi script: both succeeded.

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Codex Task

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Status	Name	Latest Commit	Preview URL	Updated (UTC)
✅ Deployment successful! View logs	gittensory-ui	e2bda37	Commit Preview URL Branch Preview URL	Jun 10 2026, 06:19 AM

[ghost]

Note

Gittensory Gate skipped

PR closed before full evaluation. No late first comment was created.

Signal	Result	Evidence	Action
Gate result	⚠️ Skipped	#488 is no longer open.	No action.

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[superagent-security]

Superagent didn't find any vulnerabilities or security issues in this PR.